Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01008913.1 Kokia drynarioides strain JFW-HI SEQ_123602, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2347
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Found at i:669 original size:3 final size:3
Alignment explanation
Indices: 656--710 Score: 58
Period size: 3 Copynumber: 18.0 Consensus size: 3
646 ACATTGTTCG
* **
656 TAA TAAA TAA TAA TAA TAA TAA TAA CT-G TTT TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
702 TAA TAA TAA
1 TAA TAA TAA
711 CATTTATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 1 0.02
3 40 0.89
4 4 0.09
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1819 original size:30 final size:30
Alignment explanation
Indices: 1783--2071 Score: 229
Period size: 30 Copynumber: 9.6 Consensus size: 30
1773 AACTATCCAA
*
1783 AAAATTATATTTTGACCCTCGAACTTCTCC
1 AAAATTATATTTTGACCCTCAAACTTCTCC
* *
1813 AAAATTATATTTTTGA-CCTCAAACTTTTCA
1 AAAATTATA-TTTTGACCCTCAAACTTCTCC
*
1843 AAAATTATATTTTGA-CCTCCAAAGTTCTCC
1 AAAATTATATTTTGACCCT-CAAACTTCTCC
* * * **
1873 AAAATTATATTTTTGACTCT-GAACTTTTTG
1 AAAATTATA-TTTTGACCCTCAAACTTCTCC
* *
1903 AAAATTACATTTTCACCCTCAAACTTCTCC
1 AAAATTATATTTTGACCCTCAAACTTCTCC
* * *
1933 AAAATTATATTTTTGA-CCTTAAACTTTTTCA
1 AAAATTATA-TTTTGACCCTCAAAC-TTCTCC
*
1964 AAAATT-TCATTTTGACCCATCAAACTTC-CTT
1 AAAATTAT-ATTTTGACCC-TCAAACTTCTC-C
*
1995 AAAATTATATTTTAACCCT-AAACTT-TCC
1 AAAATTATATTTTGACCCTCAAACTTCTCC
* * * *
2023 AAAAATTACATTTTTACCCCCAAACTT-GCC
1 -AAAATTATATTTTGACCCTCAAACTTCTCC
2053 AAAATT-TCATTTTTGACCC
1 AAAATTAT-A-TTTTGACCC
2072 GATTTTCCTA
Statistics
Matches: 207, Mismatches: 35, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
29 47 0.23
30 105 0.51
31 47 0.23
32 8 0.04
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (30 bp):
AAAATTATATTTTGACCCTCAAACTTCTCC
Found at i:1871 original size:60 final size:61
Alignment explanation
Indices: 1782--2070 Score: 328
Period size: 60 Copynumber: 4.8 Consensus size: 61
1772 AAACTATCCA
*
1782 AAAAATTATATTTTGACCCTCGAACTTCTCCAAAATTATATTTTTGACCTC-AAACTTTTC
1 AAAAATTATATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGACCTCTAAACTTTTC
* * *
1842 AAAAATTATATTTTGA-CCTCCAAAGTTCTCCAAAATTATATTTTTGA-CTCTGAACTTTTT
1 AAAAATTATATTTTGACCCT-CAAACTTCTCCAAAATTATATTTTTGACCTCTAAACTTTTC
* * *
1902 GAAAATTACATTTTCACCCTCAAACTTCTCCAAAATTATATTTTTGACCT-TAAACTTTTTC
1 AAAAATTATATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGACCTCTAAAC-TTTTC
* * *
1963 AAAAATT-TCATTTTGACCCATCAAACTTC-CTTAAAATTATA-TTTTAACC-CTAAACTTTCC
1 AAAAATTAT-ATTTTGACCC-TCAAACTTCTC-CAAAATTATATTTTTGACCTCTAAACTTTTC
* * * *
2023 AAAAATTACATTTTTACCCCCAAACTT-GCCAAAATT-TCATTTTTGACC
1 AAAAATTATATTTTGACCCTCAAACTTCTCCAAAATTAT-ATTTTTGACC
2071 CGATTTTCCT
Statistics
Matches: 195, Mismatches: 21, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
57 1 0.01
58 7 0.04
59 21 0.11
60 111 0.57
61 37 0.19
62 18 0.09
ACGTcount: A:0.34, C:0.22, G:0.04, T:0.40
Consensus pattern (61 bp):
AAAAATTATATTTTGACCCTCAAACTTCTCCAAAATTATATTTTTGACCTCTAAACTTTTC
Found at i:2085 original size:58 final size:55
Alignment explanation
Indices: 2018--2156 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 55
2008 AACCCTAAAC
*
2018 TTTCCAAAAATTA-CATTTTTACCCCCAAACTTGCC-AAAATTTCATTTTTGACCCGAT
1 TTTCCAAAAATTACCA-TTTTACCCCCAAACTT-CCAAAAATTCCATTTTTGA-CC-AT
* * * *
2075 TTTCCTAAAAATTATCATTTTACCCCCGAACTTCCAAAAATTCCATTTTTGATCTT
1 TTTCC-AAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCAT
2131 TTTCCAAAAATTACCATTTTACCCCC
1 TTTCCAAAAATTACCATTTTACCCCC
2157 GAATGTTTAA
Statistics
Matches: 74, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
55 20 0.27
56 6 0.08
57 8 0.11
58 38 0.51
59 2 0.03
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.38
Consensus pattern (55 bp):
TTTCCAAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCAT
Found at i:2187 original size:28 final size:29
Alignment explanation
Indices: 2137--2237 Score: 84
Period size: 28 Copynumber: 3.5 Consensus size: 29
2127 TCTTTTTCCA
* *
2137 AAAATTACCA-TTTTACCCCCGAATGTTT-
1 AAAATTACCATTTTTAACCACGAA-GTTTC
2165 AAAATT-CCATTTTTAACCACGAAGTTTCCC
1 AAAATTACCATTTTTAACCACGAAGTTT--C
* * * * *
2195 AAAATTACCATTTTT-CCCTCGAGGGTCC
1 AAAATTACCATTTTTAACCACGAAGTTTC
2223 AAAATTACCATTTTT
1 AAAATTACCATTTTT
2238 CCCCCCGGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
27 7 0.11
28 33 0.54
30 13 0.21
31 8 0.13
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.36
Consensus pattern (29 bp):
AAAATTACCATTTTTAACCACGAAGTTTC
Done.